Human Phenotype Ontology 
Grandparent Node:
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Aplasia/Hypoplasia of the cerebrum (HP:0007364)help
Grandparent Node:
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Decreased head circumference (HP:0040195)help
Parent Node:
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Microcephaly (HP:0000252)help
..Starting node
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Primary microcephaly (HP:0011451)help
Term ID: 11451
Name: Primary microcephaly
Synonym: Congenital decreased head circumference; Congenital microcephaly; Congenital small head; Congenital small head circumference; Congenital small skull; Decreased head circumference present at birth; Head circumference small for gestational age; Microcephaly present at birth; Small cranium present at birth; Small head circumference present at birth; Small head present at birth; Small skull present at birth
Definition: Head circumference below 2 standard deviations below the mean for age and gender at birth.
Comments:
Reference: HP:0011451
Genes and Diseases:
 
       Child Nodes:

 Sister Nodes: 
..expandProgressive microcephaly (HP:0000253) help
..expandSecondary microcephaly (HP:0005484) help
InputHPO IDHPO termDistanceGeneGene id entrezHGNC IDDiseaseIdDiseaseNameFrequencyOnsetHGMD variantsClinVar variants
 
HPO disease - gene - phenotype typical associations:
 
HPO disease - gene - phenotype less frequent non-typical associations:
HP:0011451HP:0011451Primary microcephaly0AFF3 CL E G H38996473OMIM:619297KINSSHIP SYNDROME; KINS1
HP:0011451HP:0011451Primary microcephaly0ARHGEF2 CL E G H9181682OMIM:617523Neurodevelopmental disorder with midbrain and hindbrain malformations1
HP:0011451HP:0011451Primary microcephaly0CDK5RAP2 CL E G H5575518672OMIM:604804Microcephaly 3, primary, autosomal recessive181
HP:0011451HP:0011451Primary microcephaly0CENPE CL E G H10621856OMIM:616051Microcephaly 13, primary, autosomal recessive20
HP:0011451HP:0011451Primary microcephaly0CEP63 CL E G H8025425815OMIM:614728Seckel syndrome 631
HP:0011451HP:0011451Primary microcephaly0CLPB CL E G H8157030664ORPHA:4450383-methylglutaconic aciduria type 7HP:0040281 - Very frequent38
HP:0011451HP:0011451Primary microcephaly0COG7 CL E G H9194918622ORPHA:79333COG7-CDG64
HP:0011451HP:0011451Primary microcephaly0CTNNB1 CL E G H14992514OMIM:615075Neurodevelopmental disorder with spastic diplegia and visual defects88
HP:0011451HP:0011451Primary microcephaly0CTNNB1 CL E G H14992514ORPHA:404473Severe intellectual disability-progressive spastic diplegia syndromeHP:0040282 - Frequent88
HP:0011451HP:0011451Primary microcephaly0DISC1 CL E G H271852888ORPHA:171703Microcephaly-polymicrogyria-corpus callosum agenesis syndromeHP:0040282 - Frequent2
HP:0011451HP:0011451Primary microcephaly0DTYMK CL E G H18413061OMIM:619847
HP:0011451HP:0011451Primary microcephaly0EIF5A CL E G H19843300OMIM:619376FAUNDES-BANKA SYNDROME; FABAS
HP:0011451HP:0011451Primary microcephaly0EOMES CL E G H83203372ORPHA:171703Microcephaly-polymicrogyria-corpus callosum agenesis syndromeHP:0040282 - Frequent7
HP:0011451HP:0011451Primary microcephaly0FIG4 CL E G H989616873ORPHA:3472Yunis-Varon syndromeHP:0040282 - Frequent111
HP:0011451HP:0011451Primary microcephaly0FRMD4A CL E G H5569125491OMIM:616819Corpus callosum, agenesis of, with facial anomalies and cerebellar ataxia1
HP:0011451HP:0011451Primary microcephaly0FRMD4A CL E G H5569125491ORPHA:466688Severe intellectual disability-corpus callosum agenesis-facial dysmorphism-cerebellar ataxia syndromeHP:0040282 - Frequent1
HP:0011451HP:0011451Primary microcephaly0GRIN2A CL E G H29034585ORPHA:289266Early-onset epileptic encephalopathy and intellectual disability due to GRIN2A mutationHP:0040283 - Occasional434
HP:0011451HP:0011451Primary microcephaly0GRIN2A CL E G H29034585OMIM:245570EPILEPSY, FOCAL, WITH SPEECH DISORDER AND WITH OR WITHOUT MENTAL RETARDATION; FESD434
HP:0011451HP:0011451Primary microcephaly0IFIH1 CL E G H6413518873OMIM:615846Aicardi-Goutieres syndrome 728
HP:0011451HP:0011451Primary microcephaly0KAT6A CL E G H799413013OMIM:616268Arboleda-Tham syndrome34
HP:0011451HP:0011451Primary microcephaly0KATNB1 CL E G H103006217ORPHA:89844Lissencephaly syndrome, Norman-Roberts typeHP:0040281 - Very frequent10
HP:0011451HP:0011451Primary microcephaly0LMNB2 CL E G H848236638OMIM:619180MICROCEPHALY 27, PRIMARY, AUTOSOMAL DOMINANT; MCPH2711
HP:0011451HP:0011451Primary microcephaly0MECP2 CL E G H42046990ORPHA:778Rett syndromeHP:0040284 - Very rare950
HP:0011451HP:0011451Primary microcephaly0NDE1 CL E G H5482017619ORPHA:2177HydranencephalyHP:0040283 - Occasional96
HP:0011451HP:0011451Primary microcephaly0NDE1 CL E G H5482017619OMIM:614019Lissencephaly 496
HP:0011451HP:0011451Primary microcephaly0NDE1 CL E G H5482017619ORPHA:89844Lissencephaly syndrome, Norman-Roberts typeHP:0040281 - Very frequent96
HP:0011451HP:0011451Primary microcephaly0NSF CL E G H49058016OMIM:619340DEVELOPMENTAL AND EPILEPTIC ENCEPHALOPATHY 96; DEE96
HP:0011451HP:0011451Primary microcephaly0NUP188 CL E G H2351117859OMIM:618804SANDESTIG-STEFANOVA SYNDROME; SANDSTEF4
HP:0011451HP:0011451Primary microcephaly0PDCD6IP CL E G H100158766OMIM:620047
HP:0011451HP:0011451Primary microcephaly0PHGDH CL E G H262278923ORPHA:793513-phosphoglycerate dehydrogenase deficiency, infantile/juvenile formHP:0040282 - Frequent37
HP:0011451HP:0011451Primary microcephaly0PHGDH CL E G H262278923OMIM:601815Phosphoglycerate dehydrogenase deficiency.37
HP:0011451HP:0011451Primary microcephaly0PIGH CL E G H52838964OMIM:618010Glycosylphosphatidylinositol biosynthesis defect 171
HP:0011451HP:0011451Primary microcephaly0PPFIBP1 CL E G H84969249OMIM:620024
HP:0011451HP:0011451Primary microcephaly0PPP1R15B CL E G H8491914951ORPHA:391408Primary microcephaly-mild intellectual disability-young-onset diabetes syndromeHP:0040281 - Very frequent2
HP:0011451HP:0011451Primary microcephaly0PSAT1 CL E G H2996819129ORPHA:284417Phosphoserine aminotransferase deficiency, infantile/juvenile formHP:0040281 - Very frequent27
HP:0011451HP:0011451Primary microcephaly0RBBP8 CL E G H59329891OMIM:251255Jawad syndrome68
HP:0011451HP:0011451Primary microcephaly0RELN CL E G H56499957ORPHA:89844Lissencephaly syndrome, Norman-Roberts typeHP:0040281 - Very frequent334
HP:0011451HP:0011451Primary microcephaly0RNF2 CL E G H604510061OMIM:619460LUO-SCHOCH-YAMAMOTO SYNDROME; LUSYAM
HP:0011451HP:0011451Primary microcephaly0SLC16A2 CL E G H656710923ORPHA:59Allan-Herndon-Dudley syndromeHP:0040284 - Very rare57
HP:0011451HP:0011451Primary microcephaly0SLC1A4 CL E G H650910942ORPHA:447997Spastic tetraplegia-thin corpus callosum-progressive postnatal microcephaly syndromeHP:0040282 - Frequent4
HP:0011451HP:0011451Primary microcephaly0SLC25A12 CL E G H860410982OMIM:612949Epileptic encephalopathy, early infantile, 3944
HP:0011451HP:0011451Primary microcephaly0SMC3 CL E G H91262468OMIM:610759Cornelia de Lange syndrome 391
HP:0011451HP:0011451Primary microcephaly0SPATA5 CL E G H16637818119ORPHA:457351Microcephaly-intellectual disability-sensorineural hearing loss-epilepsy-abnormal muscle tone syndromeHP:0040283 - Occasional19
HP:0011451HP:0011451Primary microcephaly0SPOP CL E G H840511254OMIM:618828NABAIS SA-DE VRIES SYNDROME, TYPE 1; NSDVS116
HP:0011451HP:0011451Primary microcephaly0STIL CL E G H649110879OMIM:612703Microcephaly 7, primary, autosomal recessive99
HP:0011451HP:0011451Primary microcephaly0TBCD CL E G H690411581ORPHA:496641Early-onset progressive diffuse brain atrophy-microcephaly-muscle weakness-optic atrophy syndromeHP:0040283 - Occasional16
HP:0011451HP:0011451Primary microcephaly0TBL1XR1 CL E G H7971829529ORPHA:487825Pierpont syndromeHP:0040282 - Frequent22
HP:0011451HP:0011451Primary microcephaly0TELO2 CL E G H989429099ORPHA:488642TELO2-related intellectual disability-neurodevelopmental disorderHP:0040281 - Very frequent12
HP:0011451HP:0011451Primary microcephaly0TPRKB CL E G H5100224259OMIM:617731Galloway-Mowat syndrome 5
HP:0011451HP:0011451Primary microcephaly0TRAPPC12 CL E G H5111224284ORPHA:500144Early-onset progressive encephalopathy-hearing loss-pons hypoplasia-brain atrophy syndromeHP:0040282 - Frequent2
HP:0011451HP:0011451Primary microcephaly0TRAPPC14 CL E G H5526225604OMIM:618351Microcephaly 25, primary, autosomal recessive
HP:0011451HP:0011451Primary microcephaly0TRIO CL E G H720412303ORPHA:476126Micrognathia-recurrent infections-behavioral abnormalities-mild intellectual disability syndromeHP:0040282 - Frequent8
HP:0011451HP:0011451Primary microcephaly0TRMT10A CL E G H9358728403OMIM:616033Microcephaly, short stature, and impaired glucose metabolism 17
HP:0011451HP:0011451Primary microcephaly0TRMT10A CL E G H9358728403ORPHA:391408Primary microcephaly-mild intellectual disability-young-onset diabetes syndromeHP:0040281 - Very frequent7
HP:0011451HP:0011451Primary microcephaly0TSEN54 CL E G H28398927561ORPHA:166063Pontocerebellar hypoplasia type 4HP:0040282 - Frequent102
HP:0011451HP:0011451Primary microcephaly0TUBB CL E G H20306820778OMIM:615771Cortical dysplasia, complex, with other brain malformations 614
HP:0011451HP:0011451Primary microcephaly0TUBB3 CL E G H1038120772ORPHA:300570Cortical dysgenesis with pontocerebellar hypoplasia due to TUBB3 mutationHP:0040283 - Occasional64
HP:0011451HP:0011451Primary microcephaly0TXN2 CL E G H2582817772ORPHA:478029Combined oxidative phosphorylation defect type 29HP:0040281 - Very frequent1
HP:0011451HP:0011451Primary microcephaly0VAC14 CL E G H5569725507ORPHA:3472Yunis-Varon syndromeHP:0040282 - Frequent6
HP:0011451HP:0011451Primary microcephaly0VPS4A CL E G H2718313488OMIM:619273CIMDAG SYNDROME; CIMDAG1
HP:0011451HP:0011451Primary microcephaly0YRDC CL E G H7969328905OMIM:619609GALLOWAY-MOWAT SYNDROME 10; GAMOS10
HP:0011451HP:0011451Primary microcephaly0ZEB2 CL E G H983914881ORPHA:261552Mowat-Wilson syndrome due to a ZEB2 point mutationHP:0040283 - Occasional362
HP:0011451HP:0011451Primary microcephaly0ZEB2 CL E G H983914881ORPHA:261537Mowat-Wilson syndrome due to monosomy 2q22HP:0040283 - Occasional362
HP:0011451HP:0011451Primary microcephaly0ZNF335 CL E G H6392515807OMIM:615095Microcephaly 10, primary, autosomal recessive60


Genes (56) :AFF3 ARHGEF2 CDK5RAP2 CENPE CEP63 CLPB COG7 CTNNB1 DISC1 DTYMK EIF5A EOMES FIG4 FRMD4A GRIN2A IFIH1 KAT6A KATNB1 LMNB2 MECP2 NDE1 NSF NUP188 PDCD6IP PHGDH PIGH PPFIBP1 PPP1R15B PSAT1 RBBP8 RELN RNF2 SLC16A2 SLC1A4 SLC25A12 SMC3 SPATA5 SPOP STIL TBCD TBL1XR1 TELO2 TPRKB TRAPPC12 TRAPPC14 TRIO TRMT10A TSEN54 TUBB TUBB3 TXN2 VAC14 VPS4A YRDC ZEB2 ZNF335

Diseases (59) :OMIM:619297 OMIM:617523 OMIM:604804 OMIM:616051 OMIM:614728 ORPHA:445038 ORPHA:79333 OMIM:615075 ORPHA:404473 ORPHA:171703 OMIM:619847 OMIM:619376 ORPHA:3472 OMIM:616819 ORPHA:466688 ORPHA:289266 OMIM:245570 OMIM:615846 OMIM:616268 ORPHA:89844 OMIM:619180 ORPHA:778 ORPHA:2177 OMIM:614019 OMIM:619340 OMIM:618804 OMIM:620047 ORPHA:79351 OMIM:601815 OMIM:618010 OMIM:620024 ORPHA:391408 ORPHA:284417 OMIM:251255 OMIM:619460 ORPHA:59 ORPHA:447997 OMIM:612949 OMIM:610759 ORPHA:457351 OMIM:618828 OMIM:612703 ORPHA:496641 ORPHA:487825 ORPHA:488642 OMIM:617731 ORPHA:500144 OMIM:618351 ORPHA:476126 OMIM:616033 ORPHA:166063 OMIM:615771 ORPHA:300570 ORPHA:478029 OMIM:619273 OMIM:619609 ORPHA:261552 ORPHA:261537 OMIM:615095
 

Human Phenotype Ontology(HPO) is developed by the Human Phenotype Ontology Consortium. The version used here is December 15 2022 release.